SMTL ID : 3r0u.1

Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Tartrate and Mg complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.192, E.220, D.245 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.192, A:E.220, A:D.245, H2O.41, H2O.111, H2O.228 MG.7: 2 residues within 4Å: Chain A: T.235, S.238 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.235, A:S.238, H2O.225, H2O.254, H2O.255, H2O.256

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: T.28, N.29, H.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:N.29 Salt bridges: A:H.30 SO4.3: 3 residues within 4Å: Chain A: K.9, T.10, R.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.10 Salt bridges: A:R.69 SO4.4: 4 residues within 4Å: Chain A: K.18, V.328, A.329, K.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.330, A:D.331 Water bridges: A:K.18 Salt bridges: A:K.18 SO4.8: 9 residues within 4Å: Chain B: T.23, I.56, K.164, D.192, N.194, D.245, K.269, C.297, M.298 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.194 Water bridges: B:S.137, B:E.220, B:D.245, B:K.269, B:K.269, B:K.269 Salt bridges: B:K.164, B:K.269 SO4.9: 5 residues within 4Å: Chain B: Y.47, K.115, G.354, F.355, N.356 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:F.355, B:N.356 Water bridges: B:K.115, B:K.115, B:K.115, B:K.351, B:G.354, B:L.357, B:A.358 Salt bridges: B:K.115 SO4.10: 3 residues within 4Å: Chain B: T.28, N.29, H.30 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:N.29, B:N.29 Salt bridges: B:H.30 SO4.11: 3 residues within 4Å: Chain B: K.18, A.329, K.330 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.330 Salt bridges: B:K.18

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.5: 9 residues within 4Å: Chain A: F.21, T.23, T.53, K.162, K.269, C.297, M.298, M.299, D.321 11 PLIP interactions: 11 interactions with chain A Water bridges: A:T.23, A:K.162, A:K.162, A:N.194, A:N.194, A:K.269, A:K.269, A:K.269 Salt bridges: A:K.162, A:K.164, A:K.269

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: F.97, F.249, D.250, K.252, D.253 Chain B: F.97, Y.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.252, A:K.252 Water bridges: A:E.246 GOL.12: 7 residues within 4Å: Chain A: F.97, Y.225 Chain B: F.97, F.249, D.250, K.252, D.253 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.252, B:D.253, A:Y.225 Water bridges: B:E.246, B:D.250, B:D.250 GOL.13: 3 residues within 4Å: Chain A: K.94 Chain B: R.26, S.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.27, B:S.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukk, T. et al., Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2011-04-06

Peptides

Enzyme of enolase superfamily: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Enzyme of enolase superfamily

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